Final Report Summary - BIOMOL. SIMULATION (Development of multi-scale molecular models, force fields and computer software for biomolecular simulation)
It was proposed to develop a next generation of molecular models, force fields, multi-resolution simulation methodology and software for biomolecular simulations which are energetically and conformationally more accurate and computationally more efficient than the state of the art in the year 2008. This goal has been achieved:
1. New GROMOS force fields 53A7, 53B7, and 53A8 have been developed and tested in free energy and polypeptide folding simulations.
2. Thermodynamically calibrated polarisable coarse-grained (CG), supra-atomic and supra-molecular models for biomolecular (co-)solvents such as water, methanol, chloroform, urea and acetone were developed and tested.
3. Polarisable atomic-level (fine-grained (FG)) and supra-atomic–level (CG) of resolution models for alkanes, alcohols, and lipids were developed.
4. A variety of new features were included in the GROMOS C++ biomolecular simulation software: (i) multi-resolution simulation for diffusive systems; (ii) simulation using damped polarisability for atoms or virtual sites; (iii) a variety of free energy calculation algorithms, e.g. EDS and OSP; (iv) methodology to compute dielectric constants from an applied field; (v) conformational search based on adiabatic decoupling of degrees of freedom in MD simulation; (vi) NMR structure refinement based on order-parameter or residual-dipolar-coupling (RDC) data; (vii) interfacing to general quantum-chemical and X-ray structure refinement software packages, to mention a few.
5. A method to compute solvation partition coefficients for solutes between different solvents was developed.
6. The envisaged development of a CG force field for proteins, and nucleic acids was abandoned in favour of the development of FG-CG force-field parameters meant for use in multi-resolution FG protein with CG solvent simulation in view of efficiency and accuracy considerations. A simple CG force field for carbohydrates was developed.
7. The GROMOS software was parallelized for use on multi-processor computers.
8. The new force fields and software features were tested and applied to a variety of biomolecular systems, see the 88 publications resulting from the research, see www.igc.ethz.ch.
9. The GROMOS manual of 1996 was expanded into nine volumes of the GROMOS software of 2011, see www.gromos.net.
1. New GROMOS force fields 53A7, 53B7, and 53A8 have been developed and tested in free energy and polypeptide folding simulations.
2. Thermodynamically calibrated polarisable coarse-grained (CG), supra-atomic and supra-molecular models for biomolecular (co-)solvents such as water, methanol, chloroform, urea and acetone were developed and tested.
3. Polarisable atomic-level (fine-grained (FG)) and supra-atomic–level (CG) of resolution models for alkanes, alcohols, and lipids were developed.
4. A variety of new features were included in the GROMOS C++ biomolecular simulation software: (i) multi-resolution simulation for diffusive systems; (ii) simulation using damped polarisability for atoms or virtual sites; (iii) a variety of free energy calculation algorithms, e.g. EDS and OSP; (iv) methodology to compute dielectric constants from an applied field; (v) conformational search based on adiabatic decoupling of degrees of freedom in MD simulation; (vi) NMR structure refinement based on order-parameter or residual-dipolar-coupling (RDC) data; (vii) interfacing to general quantum-chemical and X-ray structure refinement software packages, to mention a few.
5. A method to compute solvation partition coefficients for solutes between different solvents was developed.
6. The envisaged development of a CG force field for proteins, and nucleic acids was abandoned in favour of the development of FG-CG force-field parameters meant for use in multi-resolution FG protein with CG solvent simulation in view of efficiency and accuracy considerations. A simple CG force field for carbohydrates was developed.
7. The GROMOS software was parallelized for use on multi-processor computers.
8. The new force fields and software features were tested and applied to a variety of biomolecular systems, see the 88 publications resulting from the research, see www.igc.ethz.ch.
9. The GROMOS manual of 1996 was expanded into nine volumes of the GROMOS software of 2011, see www.gromos.net.